BeautyMcLean_Malformed_Vegetative_panicle
The paired-end sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina. The library preparation process was initiated with 200ng DNA. The DNA samples were mechanically sheared into smaller fragments by Covaris followed by continuous step of end-repair where an A is added to the 3 ends making the DNA fragments ready for adapter ligation. Following this step, platform-specific adapters are ligated to both ends of the DNA fragments. These adapters contain sequences essential for binding dual-barcoded libraries to a  flow cell for sequencing, allowing for PCR amplification of adapter-ligated fragments, and binding standard Illumina sequencing primers. To ensure maximum yields from limited amounts of starting material, a high-fidelity amplification step was performed using HiFi PCR Master Mix  The amplified libraries were analyzed in Bioanalyzer 2100 (Agilent Technologies) using High Sensitivity (HS) DNA chip as per manufacturer's instructions. After obtaining the Qubit concentration for the library and the mean peak size from Bioanalyzer profile, library were loaded onto Illumina platform for cluster generation and sequencing. Paired-End sequencing allows the template fragments to be sequenced in both the forward and reverse directions. The library molecules were bound to complementary adapter oligos on paired-end flow cell. The adapters are designed to allow selective cleavage of the forward strands after re-synthesis of the reverse strand during sequencing. The copied reverse strand was then used to sequence from the opposite end of the fragment.